One of DJ Rick's radio shout-outs mention a little boy getting his tonsils removed at Brookhaven Hospital. Brookhaven is a mental institution, not a regular hospital.
In this game is an Easter Egg in which you may visit Room 302, the main room in "Silent Hill 4: The Room." However, "Silent Hill 4: The Room" takes place in a town by the name of Ashfield; not Silent Hill. So, there is no reason Murphy should be able to visit this room while in Silent Hill. Since this is, indeed, an Easter Egg, it does not have to fit into canon.
The amount of crimes listed in the police files are far too many for a town the size of Silent Hill.
A town the size of Silent Hill is too small to warrant the installation of a subway system (which isn't there in any of the other games, anyway).
Sater says that the Devil's Pit is 490m deep, more than twice the height of the Empire State Building. The Empire State Building is 443m tall, only a 43m difference. Sater is mistaken however as the sign behind him on the observation deck states that the Pit is 531m deep, only an 88m difference.